Clay weekly context brief for the Quantitative Biology category (ISO week 2026-W39).

Clay tracks publications from the Quantitative Biology feed list. Below are recent items from this category, each with its source and a short description of what the publication covers when one is available in the source feed.

Recent publications:
1. Transcriptomic Models for Immunotherapy Response Prediction Show Limited Cross-cohort Generalisability
   Source: q-bio.GN (Genomics)
   Link: https://arxiv.org/abs/2604.05478
   Immune checkpoint inhibitors (ICIs) have transformed cancer therapy; yet substantial proportion of patients exhibit intrinsic or acquired resistance, making accurate pre-treatment response prediction a critical unmet need.
2. Intact-to-Amputee Transfer in Surface-EMG Gesture Decoding: Training Source and Calibration Budget
   Source: q-bio.NC (Neurons and Cognition)
   Link: https://arxiv.org/abs/2609.20297
   A recogniser trained on one person rarely transfers to the next, and useful performance usually demands a fresh round of labelled calibration from the end user.
3. Stability of fixed life histories to perturbation by rare diapause
   Source: q-bio.PE (Populations and Evolution)
   Link: https://arxiv.org/abs/1809.04027
   We analyze the behavior of an age-structured population subject to stochastically varying linear survival and reproduction at age-dependent rates, in the special case where births occur only when organisms attain a fixed maximum age $d$, so that generations have a constant length $d$.
4. BioPhys-Bridge: A Benchmark for Interdisciplinary Scientific Reasoning in Physics-Grounded Biological Research
   Source: q-bio.QM (Quantitative Methods)
   Link: https://arxiv.org/abs/2609.19180
   Language models face unique challenges in analyzing interdisciplinary scientific research literature.
5. Thermodynamic Space of Chemical Reaction Networks
   Source: q-bio.MN (Molecular Networks)
   Link: https://arxiv.org/abs/2407.11498
   Living systems operate out of equilibrium, continuously consuming energy to sustain organised, functional states.
6. Task- and dataset-specific information in protein language models
   Source: q-bio.BM (Biomolecules)
   Link: https://arxiv.org/abs/2608.12090
   Protein language models (PLMs) have transferred the latest advances from natural language processing to computational biology.
7. EPI-KAN: A Method For Estimating and Forecasting Time-Dependent COVID-19 Parameters
   Source: q-bio.OT (Other Quantitative Biology)
   Link: https://arxiv.org/abs/2607.15302
   We introduce EPI-KAN, a novel method for estimating COVID-19 time-varying parameters.
8. Speed and stability of segregated waves in a pressure-based model of heterogeneous cell populations
   Source: q-bio.CB (Cell Behavior)
   Link: https://arxiv.org/abs/2609.09043
   We consider a minimal pressure-based model of heterogeneous cell populations consisting of proliferative and non-proliferative cells with different mobilities.
9. Continuum modeling of fluidic and elastic flow during growth-driven wound closure in partial-EMT cell monolayers
   Source: q-bio.TO (Tissues and Organs)
   Link: https://arxiv.org/abs/2607.05820
   Large-scale circular gap closure occurs over a time scale on which cell growth and proliferation become important.
10. A robust, scalable K-statistic for quantifying immune cell clustering in spatial proteomics data
   Source: q-bio.GN (Genomics)
   Link: https://arxiv.org/abs/2412.08498
   Spatial summary statistics based on point process theory are widely used to quantify the spatial organization of cell populations in single-cell spatial proteomics data.
11. A Regional Dopamine-Serotonin Control Model of Conscious State
   Source: q-bio.NC (Neurons and Cognition)
   Link: https://arxiv.org/abs/2507.02614
   This article proposes a dopamine-serotonin theory of conscious state control.
12. Critical-like growth in non-critical transitions: linearised dynamics and epidemic applications
   Source: q-bio.PE (Populations and Evolution)
   Link: https://arxiv.org/abs/2601.14869
   In the wake of the SARS-CoV-2 pandemic, there has been heightened interest from applied mathematicians in infectious disease modelling.
13. Sharpness-Aware Minimization (SAM) Improves Classification Accuracy of Bacterial Raman Spectral Data Enabling Portable Diagnostics
   Source: q-bio.QM (Quantitative Methods)
   Link: https://arxiv.org/abs/2609.19453
   Antimicrobial resistance is expected to claim 10 million lives per year by 2050, and resource-limited regions are most affected.
14. Are You Learning Biological Signal or Shortcuts? Auditing and Mitigating Bias in Protein-Protein Interaction Datasets
   Source: q-bio.MN (Molecular Networks)
   Link: https://arxiv.org/abs/2609.10193
   Protein-protein interaction (PPI) databases do not faithfully reflect biological realities.
15. SaltyMeta: a curated benchmark and protein language model-informed web tool for salty peptide prediction
   Source: q-bio.BM (Biomolecules)
   Link: https://arxiv.org/abs/2609.16809
   Excess sodium intake remains a major public health challenge, while salty and saltiness-enhancing peptides offer a potential route to preserve sensory saltiness in reduced-sodium foods.
16. Aletheia: An Offline-First Clinical Decision Support System for Differential Diagnosis in Low-Resource Healthcare Settings
   Source: q-bio.OT (Other Quantitative Biology)
   Link: https://arxiv.org/abs/2607.24814
   Access to specialist clinical expertise remains severely limited across sub-Saharan Africa, where physician-to-patient ratios can fall below 1:25,000 in rural settings.
17. SpCAST enables scalable and interpretable integration of single-cell RNA sequencing and single-cell-resolved spatial transcriptomics
   Source: q-bio.CB (Cell Behavior)
   Link: https://arxiv.org/abs/2605.26904
   Single-cell-resolution spatial transcriptomics (scST) preserves tissue architecture but often provides targeted or sparse transcriptomic measurements, whereas scRNA-seq offers broader coverage without spatial context.
18. Democratizing Clinical Tumor Whole Genome Sequencing: 18-hour End-to-end Analysis via Trillion-parameter Large Language Models Locally Deployed on
   Source: q-bio.GN (Genomics)
   Link: https://arxiv.org/abs/2609.17620
   Whole genome sequencing (WGS) is essential for precision oncology, yet its clinical adoption remains limited by prohibitive computational costs and multi-day turnaround times.
19. Detection of spiking motifs of arbitrary length in neural activity using bounded synaptic delays
   Source: q-bio.NC (Neurons and Cognition)
   Link: https://arxiv.org/abs/2511.15296
   In the context of spiking neural networks, the temporal coding hypothesis is increasingly preferred over the rate coding hypothesis due to its advantages in processing speed and energy efficiency.
20. $\beta$-diversity and Graph Sheaf Laplacians
   Source: q-bio.PE (Populations and Evolution)
   Link: https://arxiv.org/abs/2601.17466
   We suggest an approach to measuring biodiversity based on the spectrum of graph sheaf Laplacians associated with the sample data.
21. Dynamic Generalized Gromov-Wasserstein Optimal Transport
   Source: q-bio.QM (Quantitative Methods)
   Link: https://arxiv.org/abs/2609.20008
   Gromov--Wasserstein optimal transport (GW-OT) extends classical optimal transport by introducing structure-aware transport cost.
22. Systematic pathway comparison on the powerset of rule-based biochemical systems
   Source: q-bio.MN (Molecular Networks)
   Link: https://arxiv.org/abs/2608.23180
   Computational pathway design often focuses on evaluating selected pathways or optimizing fluxes in a fixed network, but gives less direct access to the combinatorial question of which other enzyme subsets of the network can support productive alternative pathways.
23. Chamaileon: Cross-Context Binder Design with Contextualized Modeling and Mixed Sampling
   Source: q-bio.BM (Biomolecules)
   Link: https://arxiv.org/abs/2607.23518
   The rapid evolution of generative models has unlocked new potentials in protein binder design, a pivotal task in structural biology, by facilitating end-to-end generation via joint sequence-structure modeling or hallucination.
24. Conservative deterministic Markov models in mathematical biology: uniqueness of steady states, reversibility and computational methods
   Source: q-bio.OT (Other Quantitative Biology)
   Link: https://arxiv.org/abs/2608.27252
   Ordinary differential equations are commonly used throughout the sciences to build mechanistic models of time-dependent processes.
25. Antipolar Cell-cell Adhesion-causing Collective Motility Disorder
   Source: q-bio.CB (Cell Behavior)
   Link: https://arxiv.org/abs/2609.01946
   In this study, we aim to theoretically investigate antipolar cell-cell adhesion, in which adhesion sites are located on the opposite side of the leading edge of migrating cells, as a candidate for irregularly polarized adhesion that induces disorder in collective cell migration.
26. PlainMap: a lightweight, restartable mapping pipeline for ancient and modern DNA
   Source: q-bio.GN (Genomics)
   Link: https://arxiv.org/abs/2609.18372
   Mapping sequencing reads to a reference genome requires preprocessing and alignment choices that can vary with library type, fragment length, sequencing platform, and reference genome.
27. NeuroSketch: A Practical Design Recipe for Neural Decoding
   Source: q-bio.NC (Neurons and Cognition)
   Link: https://arxiv.org/abs/2512.09524
   Neural decoding is fundamental to brain-computer interfaces, with growing applications in healthcare.
28. Graph construction in QUBO-based recursive phylogenetic tree reconstruction
   Source: q-bio.PE (Populations and Evolution)
   Link: https://arxiv.org/abs/2609.16640
   Molecular sequence data are used to reconstruct evolutionary relationships among taxa, but reconstruction accuracy depends not only on the tree-building method but also on how pairwise sequence relationships are represented.
29. Hierarchical Maximum Likelihood Estimation for Time-Resolved NMR Data
   Source: q-bio.QM (Quantitative Methods)
   Link: https://arxiv.org/abs/2508.14902
   Metabolic monitoring and reaction rate estimation using hyperpolarized NMR technology requires accurate quantitative analysis of multidimensional data scenarios.
30. Uncovering Cellular Resolution in scRNAseq via Unbiased Cell and Gene Network Analysis
   Source: q-bio.MN (Molecular Networks)
   Link: https://arxiv.org/abs/2608.22982
   Conventional annotation of single-cell RNA-sequencing (scRNA-seq) data relies heavily on manual, marker-based thresholding, an approach that can obscure subtle transcriptomic gradients and collapse functionally distinct cell states into broad, heterogeneous populations.
31. Pareto-Optimal Offline Reinforcement Learning via Smooth Tchebycheff Scalarization
   Source: q-bio.BM (Biomolecules)
   Link: https://arxiv.org/abs/2604.13175
   Large language models can be aligned with human preferences through offline reinforcement learning (RL) on small labeled datasets.
32. COLD-CI: A large-scale very high-resolution label polygon dataset for cocoa and non-cocoa classification in Cote d'Ivoire
   Source: q-bio.OT (Other Quantitative Biology)
   Link: https://arxiv.org/abs/2606.20767
   Spatially explicit information on cocoa cultivation is essential for land-use planning, deforestation monitoring, environmental assessment, and supply-chain analysis.
33. Stochastic mutation as a mechanism for the emergence of SARS-CoV-2 new variants -- A Scientific Conjecture on Artificial Intelligence Paradigm
   Source: q-bio.CB (Cell Behavior)
   Link: https://arxiv.org/abs/2502.10471
   The article summaries authors' researches on spreading dynamics of COVID 19 by use of the method of continuously asking and answering questions.

Sources in this brief: q-bio.BM (Biomolecules); q-bio.CB (Cell Behavior); q-bio.GN (Genomics); q-bio.MN (Molecular Networks); q-bio.NC (Neurons and Cognition); q-bio.OT (Other Quantitative Biology); q-bio.PE (Populations and Evolution); q-bio.QM (Quantitative Methods); q-bio.TO (Tissues and Organs).
Selected 33 of 486 available items for this weekly brief.